Buggy code:
public class NanopubImpl implements Serializable , NanopubWithNs { private static final long serialVersionUID = - 1514452524339132128L ; private static final MimetypesFileTypeMap mimeMap = new MimetypesFileTypeMap ( ) ; private URI nanopubUri ; private URI headUri ; private URI assertionUri ; private URI provenanceUri ; private URI pubinfoUri ; private Set < URI > graphUris ; private Set < Statement > head ; private Set < Statement > assertion ; private Set < Statement > provenance ; private Set < Statement > pubinfo ; private List < Statement > statements = new ArrayList < > ( ) ; private List < String > nsPrefixes = new ArrayList < > ( ) ; private Map < String , String > ns = new HashMap < > ( ) ; private boolean unusedPrefixesRemoved = false ; public NanopubImpl ( Collection < Statement > statements , List < String > nsPrefixes , Map < String , String > ns ) throws MalformedNanopubException { } public NanopubImpl ( Collection < Statement > statements ) throws MalformedNanopubException { } private static final String nanopubViaSPARQLQuery = "prefix<seq2seq4repair_space>np:<seq2seq4repair_space><http:////www.nanopub.org//nschema#><seq2seq4repair_space>" + ( ( ( ( ( ( ( ( ( ( ( "prefix<seq2seq4repair_space>rdfg:<seq2seq4repair_space><http:////www.w3.org//2004//03//trix//rdfg-1//><seq2seq4repair_space>" + "prefix<seq2seq4repair_space>this:<seq2seq4repair_space><@><seq2seq4repair_space>" ) + "select<seq2seq4repair_space>?G<seq2seq4repair_space>?S<seq2seq4repair_space>?P<seq2seq4repair_space>?O<seq2seq4repair_space>where<seq2seq4repair_space>{<seq2seq4repair_space>" ) + "<seq2seq4repair_space>{<seq2seq4repair_space>" ) + "<seq2seq4repair_space>graph<seq2seq4repair_space>?G<seq2seq4repair_space>{<seq2seq4repair_space>this:<seq2seq4repair_space>a<seq2seq4repair_space>np:Nanopublication<seq2seq4repair_space>}<seq2seq4repair_space>" ) + "<seq2seq4repair_space>}<seq2seq4repair_space>union<seq2seq4repair_space>{<seq2seq4repair_space>" ) + "<seq2seq4repair_space>graph<seq2seq4repair_space>?H<seq2seq4repair_space>{<seq2seq4repair_space>this:<seq2seq4repair_space>a<seq2seq4repair_space>np:Nanopublication<seq2seq4repair_space>}<seq2seq4repair_space>.<seq2seq4repair_space>" ) + "<seq2seq4repair_space>graph<seq2seq4repair_space>?H<seq2seq4repair_space>{<seq2seq4repair_space>{<seq2seq4repair_space>this:<seq2seq4repair_space>np:hasAssertion<seq2seq4repair_space>?G<seq2seq4repair_space>}<seq2seq4repair_space>union<seq2seq4repair_space>{<seq2seq4repair_space>this:<seq2seq4repair_space>np:hasProvenance<seq2seq4repair_space>?G<seq2seq4repair_space>}<seq2seq4repair_space>" ) + "<seq2seq4repair_space>union<seq2seq4repair_space>{<seq2seq4repair_space>this:<seq2seq4repair_space>np:hasPublicationInfo<seq2seq4repair_space>?G<seq2seq4repair_space>}<seq2seq4repair_space>}<seq2seq4repair_space>" ) + "<seq2seq4repair_space>}<seq2seq4repair_space>" ) + "<seq2seq4repair_space>graph<seq2seq4repair_space>?G<seq2seq4repair_space>{<seq2seq4repair_space>?S<seq2seq4repair_space>?P<seq2seq4repair_space>?O<seq2seq4repair_space>}<seq2seq4repair_space>" ) + "}" ) ; public NanopubImpl ( Repository repo , URI nanopubUri ) throws MalformedNanopubException , RepositoryException { } public NanopubImpl ( File file , RDFFormat format ) throws IOException , MalformedNanopubException , OpenRDFException { } public NanopubImpl ( File file ) throws IOException , MalformedNanopubException , OpenRDFException { } public NanopubImpl ( URL url , RDFFormat format ) throws IOException , MalformedNanopubException , OpenRDFException { } public NanopubImpl ( URL url ) throws IOException , MalformedNanopubException , OpenRDFException { } private HttpResponse getNanopub ( URL url ) throws IOException { } public NanopubImpl ( InputStream in , RDFFormat format , String baseUri ) throws IOException , MalformedNanopubException , OpenRDFException { } public NanopubImpl ( InputStream in , RDFFormat format ) throws IOException , MalformedNanopubException , OpenRDFException { } public NanopubImpl ( String utf8 , RDFFormat format , String baseUri ) throws MalformedNanopubException , OpenRDFException { } public NanopubImpl ( String utf8 , RDFFormat format ) throws MalformedNanopubException , OpenRDFException { } private void readStatements ( InputStream in , RDFFormat format , String baseUri ) throws IOException , MalformedNanopubException , OpenRDFException { } private void init ( ) throws MalformedNanopubException { } private void collectNanopubUri ( Collection < Statement > statements ) throws MalformedNanopubException { } private void collectGraphs ( Collection < Statement > statements ) throws MalformedNanopubException { } private void addGraphUri ( URI uri ) throws MalformedNanopubException { } private void collectStatements ( Collection < Statement > statements ) throws MalformedNanopubException { } private void checkAssertion ( ) throws MalformedNanopubException { } private void checkProvenance ( ) throws MalformedNanopubException { } private void checkPubinfo ( ) throws MalformedNanopubException { if ( pubinfo . isEmpty ( ) ) { throw new MalformedNanopubException ( "Empty<seq2seq4repair_space>publication<seq2seq4repair_space>info<seq2seq4repair_space>graph" ) ; } for ( Statement st : pubinfo ) { if ( nanopubUri . equals ( st . getSubject ( ) ) ) return ; if ( nanopubUri . equals ( st . getObject ( ) ) ) return ; } <START_BUG> throw new MalformedNanopubException ( "Provenance<seq2seq4repair_space>does<seq2seq4repair_space>not<seq2seq4repair_space>refer<seq2seq4repair_space>to<seq2seq4repair_space>assertion" ) ; <END_BUG> } @ Override public URI getUri ( ) { } @ Override public URI getHeadUri ( ) { } @ Override public Set < Statement > getHead ( ) { } @ Override public URI getAssertionUri ( ) { } @ Override public Set < Statement > getAssertion ( ) { } @ Override public URI getProvenanceUri ( ) { } @ Override public Set < Statement > getProvenance ( ) { } @ Override public URI getPubinfoUri ( ) { } @ Override public Set < Statement > getPubinfo ( ) { } @ Override public Set < URI > getGraphUris ( ) { } @ Override public Calendar getCreationTime ( ) { } @ Override public Set < URI > getAuthors ( ) { } @ Override public Set < URI > getCreators ( ) { } @ Override public List < String > getNsPrefixes ( ) { } @ Override public String getNamespace ( String prefix ) { } @ Override public void removeUnusedPrefixes ( ) { } }

Fix:
throw new MalformedNanopubException ( "Publication<seq2seq4repair_space>info<seq2seq4repair_space>does<seq2seq4repair_space>not<seq2seq4repair_space>refer<seq2seq4repair_space>to<seq2seq4repair_space>nanopublication<seq2seq4repair_space>URI" ) ;